diff options
| author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-13 09:10:23 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-13 09:10:23 +1100 |
| commit | 2c92dd5c6425c67a18ab07eba7f15c07dbd4614a (patch) | |
| tree | 46be9656b500e38bd4aa47066ce8296a127dd5bf /tools/gridss-collectGridssMetrics.nix | |
| parent | 886af7beaaa98ac32db88a7453d917409cf11ae8 (diff) | |
| parent | 4574deb8e1649eaf63df424585d11645c7cfa7dd (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss-collectGridssMetrics.nix')
| -rw-r--r-- | tools/gridss-collectGridssMetrics.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix index bb8d2e9..86732b8 100644 --- a/tools/gridss-collectGridssMetrics.nix +++ b/tools/gridss-collectGridssMetrics.nix @@ -2,6 +2,7 @@ , nixpkgs , thresholdCoverage ? 10000 , flags ? null +, config ? null }: with nixpkgs; @@ -25,6 +26,7 @@ stdenv.mkDerivation rec { java -Xmx1G -cp ${bionix.gridss.jar} \ gridss.analysis.CollectGridssMetrics \ ${optionalString sorted "ASSUME_SORTED=true"} \ + ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ I=input.bam \ O=$out \ THRESHOLD_COVERAGE=${toString thresholdCoverage} |